What's not clear but is probable is that the guardian purposefully waited until we started to transform to stop the process. They probably wanted to the tadpole to alter us before "saving" us.
That seems unlikely. There’s nothing in the game to indicate that the Guardian knows that the “purifier” will actually do that. They seem to intervene when you don’t remove yourself from the machine on your own. It’s like how in Act 3 The Emperor will move you away from the upper city gate after warning you something like four times to get away from the gate because the brain is bombarding you with telepathic energy that you can’t fight off.
As far as the permanent changes, I was under the impression from the ending that everything sort of just went back to normal, which is why I say the permanent changes are my head canon.
